Align aconitate hydratase (EC 4.2.1.3) (characterized)
to candidate AO356_24390 AO356_24390 bifunctional aconitate hydratase 2/2-methylisocitrate dehydratase
Query= BRENDA::P36683
(865 letters)
>FitnessBrowser__pseudo5_N2C3_1:AO356_24390
Length = 869
Score = 1377 bits (3563), Expect = 0.0
Identities = 667/859 (77%), Positives = 761/859 (88%), Gaps = 3/859 (0%)
Query: 1 MLEEYRKHVAERAAEGIAPKPLDANQMAALVELLKNPPAGEEEFLLDLLTNRVPPGVDEA 60
+LE YRKH+ ERAA GI P+PL+A Q A L+ELLKNPPAGEE FL+DL+TNRVPPGVDEA
Sbjct: 1 VLEAYRKHIEERAALGIVPQPLNAEQTAGLIELLKNPPAGEEAFLVDLITNRVPPGVDEA 60
Query: 61 AYVKAGFLAAIAKGEAKSPLLTPEKAIELLGTMQGGYNIHPLIDALDDAKLAPIAAKALS 120
AYVKAGFL+A+AKG+A+SPLL ++A+ELLGTMQGGYNI L++ LDDA+LAP+AAK L
Sbjct: 61 AYVKAGFLSALAKGQAQSPLLDKKRAVELLGTMQGGYNIVTLVELLDDAELAPVAAKELK 120
Query: 121 HTLLMFDNFYDVEEKAKAGNEYAKQVMQSWADAEWFLNRPALAEKLTVTVFKVTGETNTD 180
HTLLMFD F+DV EKAK GN +AK V+QSWAD EWF NRP LA+K+++ VFKVTGETNTD
Sbjct: 121 HTLLMFDAFHDVAEKAKNGNVHAKAVLQSWADGEWFKNRPVLADKISLRVFKVTGETNTD 180
Query: 181 DLSPAPDAWSRPDIPLHALAMLKNAREGIEPDQPGVVGPIKQIEALQQKGFPLAYVGDVV 240
DLSPAPDAWSRPDIPLHALAMLK AR+GI PD+ G GP+KQIE ++ +GFP+AYVGDVV
Sbjct: 181 DLSPAPDAWSRPDIPLHALAMLKMARDGIVPDEQGKTGPMKQIEEMRGQGFPIAYVGDVV 240
Query: 241 GTGSSRKSATNSVLWFMGDDIPHVPNKRGGGLCLGGKIAPIFFNTMEDAGALPIEVDVSN 300
GTGSSRKSATNSVLWF GDD+P VPNKR GG C G KIAPIF+NTMEDAGALPIE DVSN
Sbjct: 241 GTGSSRKSATNSVLWFFGDDVPFVPNKRAGGFCFGSKIAPIFYNTMEDAGALPIEFDVSN 300
Query: 301 LNMGDVIDVYPYKGEVRNHETGELLATFELKTDVLIDEVRAGGRIPLIIGRGLTTKAREA 360
++MGDVID+YP+ G+V H T E+L TFE+KT VL+DEVRAGGRIPLIIGRGLT KAR
Sbjct: 301 MHMGDVIDLYPHAGKVCKHGTDEVLTTFEMKTPVLLDEVRAGGRIPLIIGRGLTEKARAE 360
Query: 361 LGLPHSDVFRQAKDVAESDRGFSLAQKMVGRACGV---KGIRPGAYCEPKMTSVGSQDTT 417
LGLP D+F++ + AES +GF+LAQKMVG+ACG+ +G+RPG YCEPKMT+VGSQDTT
Sbjct: 361 LGLPAFDLFKKPEAPAESTKGFTLAQKMVGKACGLAEGQGVRPGTYCEPKMTTVGSQDTT 420
Query: 418 GPMTRDELKDLACLGFSADLVMQSFCHTAAYPKPVDVNTHHTLPDFIMNRGGVSLRPGDG 477
GPMTRDELKDLACLGFSADLVMQSFCHTAAYPKP+DV THHTLPDFIM RGGVSLRPGDG
Sbjct: 421 GPMTRDELKDLACLGFSADLVMQSFCHTAAYPKPIDVTTHHTLPDFIMTRGGVSLRPGDG 480
Query: 478 VIHSWLNRMLLPDTVGTGGDSHTRFPIGISFPAGSGLVAFAAATGVMPLDMPESVLVRFK 537
+IHSWLNRMLLPDTVGTGGDSHTRFP+GISFPAGSGLVAFAAATGVMPLDMPES+LVRFK
Sbjct: 481 IIHSWLNRMLLPDTVGTGGDSHTRFPMGISFPAGSGLVAFAAATGVMPLDMPESILVRFK 540
Query: 538 GKMQPGITLRDLVHAIPLYAIKQGLLTVEKKGKKNIFSGRILEIEGLPDLKVEQAFELTD 597
GKM+PGITLRDLVHAIP +AI+ GLLTVEKKGKKN FSGRILEIEGL L +EQAFEL+D
Sbjct: 541 GKMKPGITLRDLVHAIPYFAIQNGLLTVEKKGKKNAFSGRILEIEGLEGLTLEQAFELSD 600
Query: 598 ASAERSAAGCTIKLNKEPIIEYLNSNIVLLKWMIAEGYGDRRTLERRIQGMEKWLANPEL 657
ASAERSAAGCTIKL+KE I EYL SNI LL+WMI EGYGD RTLERR Q ME W+ANP+L
Sbjct: 601 ASAERSAAGCTIKLSKESITEYLQSNITLLRWMIGEGYGDARTLERRAQAMEAWVANPQL 660
Query: 658 LEADADAEYAAVIDIDLADIKEPILCAPNDPDDARPLSAVQGEKIDEVFIGSCMTNIGHF 717
+EADADAEYA VI+IDLADI EP+LCAPNDPDDAR LS+V GEKIDEVFIGSCMTNIGHF
Sbjct: 661 MEADADAEYAEVIEIDLADISEPVLCAPNDPDDARLLSSVAGEKIDEVFIGSCMTNIGHF 720
Query: 718 RAAGKLLDAHKGQLPTRLWVAPPTRMDAAQLTEEGYYSVFGKSGARIEIPGCSLCMGNQA 777
RAAGKLL+ KGQLPTRLW++PPT+MDA QLTEEGYY ++GK+GAR+E+PGCSLCMGNQA
Sbjct: 721 RAAGKLLEQVKGQLPTRLWLSPPTKMDAHQLTEEGYYGIYGKAGARMEMPGCSLCMGNQA 780
Query: 778 RVADGATVVSTSTRNFPNRLGTGANVFLASAELAAVAALIGKLPTPEEYQTYVAQVDKTA 837
RV +TVVSTSTRNFPNRLG GANV+LASAELA+VA+++G+LPT EEY Y ++D A
Sbjct: 781 RVEPNSTVVSTSTRNFPNRLGDGANVYLASAELASVASILGRLPTVEEYMEYAGKIDSMA 840
Query: 838 VDTYRYLNFNQLSQYTEKA 856
D YRYL+F+Q++++ E A
Sbjct: 841 ADVYRYLSFDQIAEFREAA 859
Lambda K H
0.317 0.136 0.400
Gapped
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 1
Number of Hits to DB: 2150
Number of extensions: 76
Number of successful extensions: 2
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 865
Length of database: 869
Length adjustment: 42
Effective length of query: 823
Effective length of database: 827
Effective search space: 680621
Effective search space used: 680621
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 56 (26.2 bits)
Align candidate AO356_24390 AO356_24390 (bifunctional aconitate hydratase 2/2-methylisocitrate dehydratase)
to HMM TIGR00117 (acnB: aconitate hydratase 2 (EC 4.2.1.3))
# hmmsearch :: search profile(s) against a sequence database
# HMMER 3.3.1 (Jul 2020); http://hmmer.org/
# Copyright (C) 2020 Howard Hughes Medical Institute.
# Freely distributed under the BSD open source license.
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# query HMM file: ../tmp/path.carbon/TIGR00117.hmm
# target sequence database: /tmp/gapView.6088.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Query: TIGR00117 [M=844]
Accession: TIGR00117
Description: acnB: aconitate hydratase 2
Scores for complete sequences (score includes all domains):
--- full sequence --- --- best 1 domain --- -#dom-
E-value score bias E-value score bias exp N Sequence Description
------- ------ ----- ------- ------ ----- ---- -- -------- -----------
0 1527.1 0.0 0 1526.9 0.0 1.0 1 lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_24390 AO356_24390 bifunctional aconita
Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_24390 AO356_24390 bifunctional aconitate hydratase 2/2-methylisocitrate deh
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 1526.9 0.0 0 0 1 844 [] 1 857 [. 1 857 [. 0.99
Alignments for each domain:
== domain 1 score: 1526.9 bits; conditional E-value: 0
TIGR00117 1 lleeyrkhvaeraaegiaplplnakqvaalvellkndpeaeeefllellidrvppgvdeaayv 63
+le+yrkh+ eraa+gi p+plna+q+a l+ellkn+p++ee+fl++l+++rvppgvdeaayv
lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_24390 1 VLEAYRKHIEERAALGIVPQPLNAEQTAGLIELLKNPPAGEEAFLVDLITNRVPPGVDEAAYV 63
69************************************************************* PP
TIGR00117 64 kagflaaiakgevksplisaeeavellgtmlggynvepliealeskdkniakaaakalsktll 126
kagfl+a+akg+++spl+ ++avellgtm+ggyn+ +l+e+l+ d+++a++aak l++tll
lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_24390 64 KAGFLSALAKGQAQSPLLDKKRAVELLGTMQGGYNIVTLVELLD--DAELAPVAAKELKHTLL 124
********************************************..***************** PP
TIGR00117 127 vfdafddveelskt.neyakqvleswaeaewflnkeelaekitvtvfkvdgetntddlspapd 188
+fdaf+dv+e++k n +ak vl+swa++ewf n++ la+ki+ vfkv+getntddlspapd
lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_24390 125 MFDAFHDVAEKAKNgNVHAKAVLQSWADGEWFKNRPVLADKISLRVFKVTGETNTDDLSPAPD 187
************998************************************************ PP
TIGR00117 189 aftrpdiplhalamlknkieeieq..........rikalkqkgvpvayvgdvvgtgssrksat 241
a++rpdiplhalamlk ++++i + +i++++ +g+p+ayvgdvvgtgssrksat
lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_24390 188 AWSRPDIPLHALAMLKMARDGIVPdeqgktgpmkQIEEMRGQGFPIAYVGDVVGTGSSRKSAT 250
*********************999999************************************ PP
TIGR00117 242 nsvlwflgkdipfvpnkragglvlggkiapiffntaedsgalpievdvkdlnegdvikiypyk 304
nsvlwf+g+d+pfvpnkragg+++g kiapif+nt+ed+galpie dv+++++gdvi++yp+
lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_24390 251 NSVLWFFGDDVPFVPNKRAGGFCFGSKIAPIFYNTMEDAGALPIEFDVSNMHMGDVIDLYPHA 313
*************************************************************** PP
TIGR00117 305 geitnket.evvatfklkpetlldevraggripliigrgltdkarealglsesevfkkakapa 366
g++ ++ t ev++tf++k+ +lldevraggripliigrglt+kar lgl+ ++fkk++apa
lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_24390 314 GKVCKHGTdEVLTTFEMKTPVLLDEVRAGGRIPLIIGRGLTEKARAELGLPAFDLFKKPEAPA 376
******9999***************************************************** PP
TIGR00117 367 esakgftlaqklvgkacgv...kgirpgtycepkvttvgsqdttgamtrdelkelaslgfdad 426
es+kgftlaqk+vgkacg+ +g+rpgtycepk+ttvgsqdttg+mtrdelk+la+lgf+ad
lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_24390 377 ESTKGFTLAQKMVGKACGLaegQGVRPGTYCEPKMTTVGSQDTTGPMTRDELKDLACLGFSAD 439
******************86668**************************************** PP
TIGR00117 427 lvlqsfchtaaypkpvdvkthktlpdfisqrggvalrpgdgvihswlnrmllpdtvgtggdsh 489
lv+qsfchtaaypkp+dv th+tlpdfi++rggv+lrpgdg+ihswlnrmllpdtvgtggdsh
lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_24390 440 LVMQSFCHTAAYPKPIDVTTHHTLPDFIMTRGGVSLRPGDGIIHSWLNRMLLPDTVGTGGDSH 502
*************************************************************** PP
TIGR00117 490 trfplgisfpagsglvafaaatgvmpldmpesvlvrfkgelqpgitlrdlvnaipyyaikkgl 552
trfp+gisfpagsglvafaaatgvmpldmpes+lvrfkg+++pgitlrdlv+aipy+ai++gl
lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_24390 503 TRFPMGISFPAGSGLVAFAAATGVMPLDMPESILVRFKGKMKPGITLRDLVHAIPYFAIQNGL 565
*************************************************************** PP
TIGR00117 553 ltvekkgkvnvfngrileieglpdlkveqafeltdasaersaagctiklnkepvieylksniv 615
ltvekkgk+n f+grileiegl l +eqafel+dasaersaagctikl+ke++ eyl+sni
lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_24390 566 LTVEKKGKKNAFSGRILEIEGLEGLTLEQAFELSDASAERSAAGCTIKLSKESITEYLQSNIT 628
*************************************************************** PP
TIGR00117 616 llkemiaegyedkrtlkrridamekwlanpelleadadaeyaavieidlaeikepilaapndp 678
ll++mi egy+d+rtl+rr +ame+w+anp+l+eadadaeya+vieidla+i ep+l+apndp
lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_24390 629 LLRWMIGEGYGDARTLERRAQAMEAWVANPQLMEADADAEYAEVIEIDLADISEPVLCAPNDP 691
*************************************************************** PP
TIGR00117 679 ddvkllsevagdaidevfigscmtnighfraagkileaak.tvkarlwvvpptrmdeqqliee 740
dd++lls vag++idevfigscmtnighfraagk+le+ k ++++rlw+ ppt+md++ql+ee
lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_24390 692 DDARLLSSVAGEKIDEVFIGSCMTNIGHFRAAGKLLEQVKgQLPTRLWLSPPTKMDAHQLTEE 754
*************************************9988********************** PP
TIGR00117 741 gyyaifgaagartevpgcslcmgnqarvedgatvfststrnfdnrlgkgakvylgsaelaava 803
gyy+i+g+agar+e+pgcslcmgnqarve ++tv+ststrnf+nrlg ga+vyl+saela+va
lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_24390 755 GYYGIYGKAGARMEMPGCSLCMGNQARVEPNSTVVSTSTRNFPNRLGDGANVYLASAELASVA 817
*************************************************************** PP
TIGR00117 804 allgkiptkeeylalvsekvesakdklyrylnfnelenfee 844
++lg++pt+eey+++ + + a d +yryl f+++ +f+e
lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_24390 818 SILGRLPTVEEYMEYAGKIDSMAAD-VYRYLSFDQIAEFRE 857
***************8877766666.************985 PP
Internal pipeline statistics summary:
-------------------------------------
Query model(s): 1 (844 nodes)
Target sequences: 1 (869 residues searched)
Passed MSV filter: 1 (1); expected 0.0 (0.02)
Passed bias filter: 1 (1); expected 0.0 (0.02)
Passed Vit filter: 1 (1); expected 0.0 (0.001)
Passed Fwd filter: 1 (1); expected 0.0 (1e-05)
Initial search space (Z): 1 [actual number of targets]
Domain search space (domZ): 1 [number of targets reported over threshold]
# CPU time: 0.07u 0.03s 00:00:00.10 Elapsed: 00:00:00.09
# Mc/sec: 8.09
//
[ok]
This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory